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@STRING{ABio = {Analytical Biochemistry}}

@STRING{ACMTG = {ACM Transactions on Graphics}}

@STRING{ACMTMS = {ACM Transactions on Mathematical Software}}

@STRING{AJB = {American Journal of Botany}}

@STRING{AJM = {American Journal of Mathematics}}

@STRING{AJPh = {American Journal of Physiology}}

@STRING{ANM = {Applied Numerical Mathematics}}

@STRING{AoB = {Annals of Botany}}

@STRING{ARBE = {Annual Review of Biomedical Engineering}}

@STRING{ARCDB = {Annual Review Cell Development Biology}}

@STRING{ARG = {Annual Review of Genetics}}

@STRING{ARPB = {Annual Review of Plant Biology}}

@STRING{ARPPPMB = {Annual review of Plant Physiology and Plant Molecular biology}}

@STRING{ASBP = {Acta Societatis Botanicorum Poloniae}}

@STRING{ASN = {Annales des Sciences Naturelles}}

@STRING{BCG = {Biochemical Genetics}}

@STRING{Bioinf = {Bioinformatics}}

@STRING{BioJ = {Biophysical Journal}}

@STRING{BMB = {Bulletin of Mathematical Biology}}

@STRING{BPChem = {Biophysical Chemistry}}

@STRING{BTech = {BioTechniques}}

@STRING{BVSQ = {Binocul Vis Strabismus Q}}

@STRING{BZ = {Botanical Gazette}}

@STRING{CAGD = {Computer Aided Geometric Design}}

@STRING{CB = {Current Biology}}

@STRING{CDiff = {Cell Differentiation}}

@STRING{CG = {Computer Graphics}}

@STRING{CGIM = {Computer Graphics and Image Processing}}

@STRING{CGTA = {Computational Geometry: Theory and Applications}}

@STRING{CJB = {Canadian Journal of Botany}}

@STRING{CJC = {The Canadian Journal of Cardiology }}

@STRING{CJPP = {Canadian Journal of Physiology and Pharmacology}}

@STRING{COCB = {Current Opinion in Cell Biology}}

@STRING{COGD = {Current Opinion in Genetics \& Development}}

@STRING{COPB = {Current Opinion in Plant Biology}}

@STRING{CRB = {Comptes Rendus Biologies}}

@STRING{CSHPB = {Cold Spring Harbor Perspectives in Biology}}

@STRING{CSSP = {Circuits, Systems and Signal Processing}}

@STRING{CSurv = {Computing Survey}}

@STRING{CurBio = {Current Biology}}

@STRING{DevBio = {Developmental Biology}}

@STRING{DevCell = {Developmental Cell}}

@STRING{DevDyn = {Developmental Dynamics}}

@STRING{DevGen = {Developmental Genetics}}

@STRING{DevSupp = {Development Supplement}}

@STRING{EJOR = {European Journal of Operational Research}}

@STRING{EMBOJ = {The EMBO Journal}}

@STRING{ENTCS = {Electronic Notes in Theoretical Computer Science}}

@STRING{GDev = {Genes and Development}}

@STRING{GI = {Graphics Interface}}

@STRING{GMIP = {Graphical models and image processing}}

@STRING{ICSE = {IMPACT of Computing in Science and Engineering }}

@STRING{IEEEAC = {IEEE Transactions on Automatic Control}}

@STRING{IEEETMI = {IEEE Transactions on Medical Imaging}}

@STRING{IEEETPAMI = {IEEE Transactions on Pattern Analysis and Machine Intelligence}}

@STRING{IEEETVCG = {IEEE Transactions on Visualization and Computer Graphics}}

@STRING{IJDB = {International Journal of Developmental Biology}}

@STRING{IJORMD = {International Journal of Obesity and Related Metabolic Disorders}}

@STRING{IJPS = {International Journal of the Plant Sciences}}

@STRING{IJSM = {International Journal of Shape Modeling}}

@STRING{IRC = {International Review of Cytology}}

@STRING{JBC = {The Journal of Biological Chemistry}}

@STRING{JBCB = {Journal of Bioinformatics and Computational Biology}}

@STRING{JCardPh = {Journal of Cardiovascular Pharmacology}}

@STRING{JCB = {Journal of Cell Biology}}

@STRING{JCC = {Journal of Computational Chemistry}}

@STRING{JChP = {Journal of Chemical Physics}}

@STRING{JCP = {Journal of Computational Physics}}

@STRING{JCS = {Journal of Cell Science}}

@STRING{JEB = {Journal of Experimental Botany}}

@STRING{JGAA = {Journal of Graph Algorithms and Applications}}

@STRING{JHC = {The Journal of Histochemistry and Cytochemistry}}

@STRING{JMB = {Journal of Mathematical Biology}}

@STRING{JMemB = {The Journal of Membrane Biology}}

@STRING{JMS = {Journal of Manufacturing Systems}}

@STRING{JPGR = {Journal of Plant Growth Regulation}}

@STRING{JraM = {Journal f\"{u}r die reine und angewandte Mathematik}}

@STRING{JRSI = {Journal of the Royal Society Interface}}

@STRING{JSC = {Journal of Scientific Computing}}

@STRING{JTB = {Journal of Theoretical Biology}}

@STRING{JVCIR = {Journal of Visual Communication and Image Representation}}

@STRING{LNCS = {Lecture Notes in Computer Science}}

@STRING{MBE = {Molecular Biology and Evolution}}

@STRING{MGG = {Molecular Genetics and Genomics}}

@STRING{ModHealth = {Modern Healthcare}}

@STRING{MolM = {Molecular Microbiology}}

@STRING{MSB = {Molecular System Biology}}

@STRING{NAACLC = {Nova Acta Academiae Caesareae Leopoldino Carolinae Germanicae Naturae
	Curiosorum}}

@STRING{NAMS = {Notice of the American Mathematical Society}}

@STRING{NPhyt = {New Phytologist}}

@STRING{NRG = {Nature Reviews Genetics}}

@STRING{NRMCB = {Nature Reviews: Molecular Cell Biology}}

@STRING{PatRec = {Pattern Recognition}}

@STRING{PCCP = {Physical Chemistry Chemical Physics}}

@STRING{PCE = {Plant, Cell and Environment}}

@STRING{PCP = {Plant Cell Physiology}}

@STRING{PhysB = {Physical Biology}}

@STRING{PhysD = {Physica D (Nonlinear Phenomena)}}

@STRING{PIEEE = {Proceedings of the IEEE}}

@STRING{PLOSBio = {PLOS Biology}}

@STRING{PLOSCB = {PLOS Computational Biology}}

@STRING{PMB = {Plant Molecular Biology}}

@STRING{PNAS = {Proceedings of the National Academy of Science of the USA}}

@STRING{PPh = {Plant Physiology}}

@STRING{PRL = {Physical Review Letters}}

@STRING{Prot = {Protoplasma}}

@STRING{PRSLB = {Proceesings of the Royal Society of London: Series B, Biological
	Sciences}}

@STRING{RPP = {Reports of Progress in Physics}}

@STRING{RSLBS = {Philosophical Transactions of the Royal Society of London. B. Biological
	Sciences}}

@STRING{SCDB = {Seminars in Cell and Developmental Biology}}

@STRING{SHort = {Scientia Horticulturae}}

@STRING{SIAMJAM = {SIAM Journal on Applied Mathematic}}

@STRING{SIAMJC = {SIAM Journal on Computing}}

@STRING{SIAMJMAA = {SIAM Journal on Matrix Analysis and Applications}}

@STRING{SIAMJNA = {SIAM Journal on Numerical Analysis}}

@STRING{SIGGRAPHCG = {SIGGRAPH Computer Graphics}}

@STRING{SProc = {Signal Processing}}

@STRING{SSEB = {Symposia of the Society for Experimental Biology}}

@STRING{TBS = {Trends in Biochemical Sciences}}

@STRING{TIG = {Trends in Genetics}}

@STRING{TPC = {The Plant Cell}}

@STRING{TPJ = {The Plant Journal}}

@STRING{TPS = {Trends in Plant Science}}

@INPROCEEDINGS{Cabral93,
  author = {Cabral, Brian and Leedom, Leith Casey},
  title = {Imaging vector fields using line integral convolution},
  booktitle = {Proceedings of the 20th annual conference on Computer graphics and
	interactive techniques},
  year = {1993},
  number = {263--270},
  publisher = {ACM Press},
  crossref = {ISBN:0-89791-601-8},
  file = {Cabral93.pdf:info/Cabral93.pdf:PDF},
  owner = {barbierp},
  timestamp = {2009.02.17}
}

@INPROCEEDINGS{Does83,
  author = {de Does, Mark and Lindenmayer, Aristide},
  title = {Algorithms for the generation and drawing of maps representing cell
	clones.},
  year = {1983},
  crossref = {Ehrig83},
  owner = {barbierp},
  timestamp = {2009.05.05}
}

@INPROCEEDINGS{Fracchia96,
  author = {Fracchia, F. David},
  title = {Integrating Lineage and Interaction for the Visualization of Cellular
	Stuctures},
  year = {1996},
  pages = {521-535},
  bibsource = {DBLP, http://dblp.uni-trier.de},
  crossref = {Cuny96}
}

@ARTICLE{Goldman02,
  author = {Goldman, Ron},
  title = {On the algebraic and geometric foundations of computer graphics},
  journal = ACMTG,
  year = {2002},
  volume = {21},
  pages = {52--86},
  number = {1},
  month = jan,
  abstract = {Today’s computer graphics is ostensibly based upon insights from projective
	geometry and computations on homogeneous coordinates. Paradoxically,
	however, projective spaces and homogeneous coordinates are incompatible
	with much of the algebra and a good deal of the geometry currently
	in actual use in computer graphics. To bridge this gulf between theory
	and practice, Grassmann spaces are proposed here as an alternative
	to projective spaces. We establish that unlike projective spaces,
	Grassmann spaces do support all the algebra and geometry needed for
	contemporary computer graphics. We then go on to explain how to exploit
	this algebra and geometry for a variety of applications, both old
	and new, including the graphics pipeline, shading algorithms, texture
	maps, and overcrown surfaces.},
  crossref = {ISSN:0730-0301},
  doi = {10.1145/504789.504792},
  file = {Goldman02.pdf:info/Goldman02.pdf:PDF},
  keywords = {Algorithms, Theory, Grassmann space, homogeneous coordinates, mass-points,
	projective space},
  owner = {barbierp},
  timestamp = {2009.11.13}
}

@ARTICLE{Kennedy88,
  author = {Kennedy, D. P.},
  title = {A Note on Stochastic Search Methods for Global Optimization},
  journal = {Advances in Applied Probability},
  year = {1988},
  volume = {20},
  pages = {476--478},
  number = {2},
  month = Jun,
  abstract = {Let [An,Bn] be random subintervals of [0, 1] defined recursively as
	follows. Let A1=0,B1=1 and take Cn,Dn to be the minimum and maximum
	of k, i.i.d. random points uniformly distributed on [An,Bn]. Choose
	[An+1,Bn+1] to be [Cn,Bn],[An,Dn] or [Cn,Dn] with probabilities p,q,r
	respectively, p+q+r=1. It is shown that the limiting distribution
	of [An,Bn] has the beta distribution on [0, 1] with parameters k(p+r)
	and k(q+r). The result is used to consider a randomized version of
	Golden Section search},
  bdsk-url-1 = {http://www.jstor.org/stable/1427401},
  crossref = {00018678},
  file = {Kennedy88.pdf:math/stochastic_methods/Kennedy88.pdf:PDF},
  owner = {barbierp},
  timestamp = {2009.03.10},
  url = {http://www.jstor.org/stable/1427401}
}

@INBOOK{Launchbury95,
  chapter = {Graph algorithms with a functional flavour},
  pages = {308--331},
  title = {Advanced Functional Programming},
  publisher = {Springer Berlin / Heidelberg},
  year = {1995},
  author = {John Launchbury},
  volume = {925},
  crossref = {ISBN=978-3-540-59451-2},
  doi = {10.1007/3-540-59451-5_9},
  file = {Launchbury95.pdf:info/Launchbury95.pdf:PDF},
  owner = {pbdr},
  timestamp = {2010.05.04}
}

@INPROCEEDINGS{Luck82,
  author = {Jacqueline L{\"u}ck and Hermann B. L{\"u}ck},
  title = {Generation of 3-dimensional plant bodies by double wall map and stereomap
	systems},
  booktitle = {Graph Grammars Workshops},
  year = {1982},
  pages = {219-231},
  bibsource = {DBLP, http://dblp.uni-trier.de},
  crossref = {DBLP:conf/gg/1982}
}

@BOOK{Murray89,
  title = {Mathematical Biology},
  publisher = {Springer-Verlqg},
  year = {1989},
  editor = {Levin, S. A.},
  author = {Murray, James D.},
  volume = {19},
  series = {Biomathematics Texts},
  crossref = {ISBN 3-540-19640-6 , ISBN 0-387-19460-6},
  owner = {barbier},
  review = {Mathematical Biology, with its 292 figures, is an unusually richly
	illustrated textbook of this fast growing field. It gives an in-depth
	account of the pratical use of mathematical modelling in many important
	and diverse areas of the bio-sciences. The emphasis is on what is
	required to solve real biological problems.
	
	The subject matter is drawn from such topics as population biology,
	biological oscillators, the Belousov-Zhabotinskii reaction, biological
	wave phenomena, developmental biology, the new mechanochemical theory
	of embryolofical pattern formation, neural models and the spread
	of epidemics.
	
	The book provides a thorough training in pratical mathematical biology
	and show how exciting and new mathemarical challenges can arise from
	a genuinely interdisciplinary involvement with the biosciences. It
	also shows how mathematics can contribute to biology and why physical
	scientists should get involved - and how to do so.
	
	The book present a broad view of the field of theoretical and mathematical
	biology and gives an excellent background from which to begin genuine
	interdisciplinary research in the biomedical sciences.},
  timestamp = {2007.12.05}
}

@ARTICLE{Poincare1890,
  author = {Poincaré, Henri},
  title = {Sur le probléme des trois corps et les équations de la dynamique},
  journal = {Acta Mathematica},
  year = {1890},
  volume = {13},
  pages = {A3--A270},
  number = {1},
  month = Dec,
  crossref = {0001-5962 (Print) 1871-2509 (Online)},
  doi = {10.1007/BF02392506},
  file = {:math/Pointcare1890.pdf:PDF},
  keywords = {dynamic system},
  owner = {pbdr},
  timestamp = {2010.05.31}
}

@ARTICLE{Rossl11,
  author = {R\"{o}ssl, Christian and Theisel, Holger},
  title = {Streamline Embedding for 3D Vector Field Exploration},
  journal = IEEETVCG,
  year = {2011},
  month = Apr,
  abstract = {We propose a new technique for visual exploration of streamlines in
	3D vector ﬁelds. We construct a map from the space of all streamlines
	to points in IRn based on the preservation of the Hausdorff metric
	in streamline space. The image of a vector ﬁeld under this map is
	a set of 2-manifolds in IRn with characteristic geometry and topology.
	Then standard clustering methods applied to the point sets in IRn
	yield a segmentation of the original vector ﬁeld. Our approach provides
	a global analysis of 3D vector ﬁelds which incorporates the topological
	segmentation but yields additional information. In addition to a
	pure segmentation, the established map provides a natural “parametrization”
	visualized by the manifolds. We test our approach on a number of
	synthetic and real-world data
	
	sets.},
  crossref = {ISSN: 1077-2626},
  doi = {10.1109/TVCG.2011.78},
  file = {Rossl11.pdf:prog/geometry/Rossl11.pdf:PDF},
  keywords = {vector ﬁelds, streamline embedding, clustering},
  owner = {barbier},
  timestamp = {2011.05.05}
}

@ARTICLE{Rother04,
  author = {Rother, Carsten and Kolmogorov, Vladimir and Blake, Andrew},
  title = {Interactive foreground extraction using iterated graph cuts},
  journal = ACMTG,
  year = {2004},
  volume = {23},
  pages = {309--314},
  number = {3},
  abstract = {The problem of efficient, interactive foreground/background segmentation
	in still images is of great practical importance in image editing.
	Classical image segmentation tools use either texture (colour) information,
	e.g. Magic Wand, or edge (contrast) information, e.g. Intelligent
	Scissors. Recently, an approach based on optimization by graph-cut
	has been developed which successfully combines both types of information.
	In this paper we extend the graph-cut approach in three respects.
	First, we have developed a more powerful, iterative version of the
	optimisation. Secondly, the power of the iterative algorithm is used
	to simplify substantially the user interaction needed for a given
	quality of result. Thirdly, a robust algorithm for ``border matting''
	has been developed to estimate simultaneously the alpha-matte around
	an object boundary and the colours of foreground pixels. We show
	that for moderately difficult examples the proposed method outperforms
	competitive tools.},
  crossref = {I.3.3 [Computer Graphics]: Picture/Image Generation - Display algorithms;
	I.3.6 [Computer Graphics]: Methodology and Techniques - Interaction
	techniques; I.4.6 [Image Processing and Computer Vision]: Segmentation
	- Pixel classification; partitioning},
  file = {:math/image/Rother04.pdf:PDF},
  keywords = {Interactive Image Segmentation, Graph Cuts, Image Editing, Foreground
	extraction, Alpha Matting},
  owner = {barbier},
  timestamp = {2006.05.10}
}

@INPROCEEDINGS{Singh04,
  author = {Harbir Singh and Michael Crawford and John Curtin and Reyer Zwiggelaar},
  title = {Automated {3D} segmentation of the lung airway tree using gain-based
	region growing approach},
  booktitle = {Medical Image Computing and Computer-Assisted Intervention - MICCAI
	2004},
  year = {2004},
  editor = {Barillot, Christian and Haynor, David R. and Hellier, Pierre},
  volume = {3217},
  series = {Lecture Notes in Computer Science},
  pages = {975--982},
  month = Sep,
  publisher = {Springer Berlin / Heidelberg},
  abstract = {In diagnosing lung diseases, it is highly desirable to be able to
	segment the lung into physiological structures, such as the intra-thoracic
	airway tree and the pulmonary structure. Providing an in-vivo and
	non-invasive tool for 3D reconstruction of anatomical tree structures
	such as the bronchial tree from 2D and 3D data acquisitions is a
	challenging issue for computer vision in medical imaging. Due to
	the complexity of the tracheobronchial tree, the segmentation task
	is non trivial. This paper describes a 3D adaptive region growing
	algorithm incorporating gain calculation for segmenting the primary
	airway tree using a stack of 2D CT slices. The algorithm uses an
	entropy-based measure known as information gain as a heuristic for
	selecting the voxels that are most likely to represent the airway
	regions.},
  crossref = {ISBN: 978-3-540-22977-3},
  file = {:math/image/Singh04.pdf:PDF},
  owner = {pbarbier},
  timestamp = {2006.12.14}
}

@TECHREPORT{Abrahams03,
  author = {Abrahams, David},
  title = {Building hybrid systems with {Boost.Python}},
  institution = {Boost Consulting},
  year = {2003},
  abstract = {Boost.Python is an open source C++ library which provides a concise
	IDL-like interface for binding C++ classes and functions to Python.
	Leveraging the full power of C++ compile-time introspection and of
	recently developed metaprogramming techniques, this is achieved entirely
	in pure C++, without introducing a new syntax. Boost.Python's rich
	set of features and high-level interface make it possible to engineer
	packages from the ground up as hybrid systems, giving programmers
	easy and coherent access to both the efficient compile-time polymorphism
	of C++ and the extremely convenient run-time polymorphism of Python.},
  bdsk-url-1 = {http://www.boost-consulting.com/writing/bpl.html},
  file = {:prog/python/Abrahams03.txt:PDF},
  url = {http://www.boost-consulting.com/writing/bpl.html}
}

@ARTICLE{Adler75,
  author = {Adler, Irving},
  title = {A model of space filling in phyllotaxis},
  journal = JTB,
  year = {1975},
  volume = {53},
  pages = {435--444},
  owner = {barbier}
}

@ARTICLE{Adler74,
  author = {Adler, Irving},
  title = {A model of contact pressure in phyllotaxis},
  journal = JTB,
  year = {1974},
  volume = {45},
  pages = {1--79},
  owner = {barbier}
}

@ARTICLE{Adler97,
  author = {Adler, Irving and Barabe, D. and Jean, R. V.},
  title = {A history of the study of phyllotaxis},
  journal = AOB,
  year = {1997},
  volume = {80},
  pages = {231--244},
  number = {3},
  month = Sep,
  abstract = {The study of the patterns formed by similar units in plants (e.g.
	leaves, scales, florets) is traced from the first primitive observations
	in ancient times to the sophisticated studies of today. Mathematics
	entered into the study early, at first as a way of describing the
	patterns observed, with Fibonacci numbers and the golden section
	playing a major role, and later in the construction of models designed
	to explain their origin. Observation and experiment alternated with
	theory. Explanations offered alternated between functional and causal.
	Functional explanations that were at first teleological gave way
	to those based on the idea of natural selection. Causal explanations
	alternated between the chemical and the mechanical. New light has
	been cast on the subject with the realization that phenomena similar
	to phyllotaxis occur in realms outside of botany.},
  bdsk-url-1 = {http://dx.doi.org/10.1006/anbo.1997.0422},
  doi = {10.1006/anbo.1997.0422},
  file = {:biology/phyllotaxy/Adler97.pdf:PDF},
  keywords = {Phyllotaxis; genes; algae; comparative morphology; evolutionary theory;
	systems research; optimal design; polypeptide chains; living crystals;
	allometry},
  timestamp = {2005.09.20}
}

@ARTICLE{Adler02,
  author = {Paul N Adler},
  title = {Planar signaling and morphogenesis in Drosophila.},
  journal = DevCell,
  year = {2002},
  volume = {2},
  pages = {525--535},
  number = {5},
  month = May,
  abstract = {The regulatory mechanisms governing the parallel alignment of hairs,
	bristles, and ommatidia in Drosophila have all served as model systems
	for studying planar signaling and tissue level morphogenesis. Polarity
	in all three systems is mediated by the serpentine receptor Frizzled
	and a number of additional gene products. The localized accumulation
	of these proteins within cells plays a key role in the development
	of planar polarity. A comparison of the function of these gene products
	in the different cell types suggests cell-specific modifications
	of the pathway.},
  doi = {10.1016/S1534-5807(02)00176-4},
  file = {Adler02.pdf:biology/Adler02.pdf:PDF},
  institution = {, USA. pna@virginia.edu},
  keywords = {Animals; Body Patterning, physiology; Cytoskeleton, physiology; Drosophila
	Proteins, genetics/physiology; Drosophila, genetics/growth /&/ development/physiology;
	Epidermis, growth /&/ development; Frizzled Receptors; Genes, Insect;
	Membrane Proteins, genetics/physiology; Models, Biological; Mutation;
	Phenotype; Receptors, G-Protein-Coupled; Signal Transduction, physiology;
	Wing, growth /&/ development; PCP},
  language = {eng},
  medline-pst = {ppublish},
  owner = {barbierp},
  pii = {S1534580702001764},
  pmid = {12015961},
  timestamp = {2010.08.06}
}

@ARTICLE{Adler01,
  author = {P. N. Adler and H. Lee},
  title = {Frizzled signaling and cell-cell interactions in planar polarity.},
  journal = COCB,
  year = {2001},
  volume = {13},
  pages = {635--640},
  number = {5},
  month = Oct,
  abstract = {The function of the Frizzled pathway is essential for the formation
	of the array of distally pointing hairs found on the Drosophila wing.
	Previous research found that regulating the subcellular location
	for hair initiation controlled hair polarity. Recent work argues
	a graded Frizzled-dependent signal results in the accumulation of
	the Frizzled, Dishevelled and Flamingo proteins along the distal
	edge of the wing cells. This cortical mark leads to the local activation
	of downstream gene products and the subsequent activation of the
	cytoskeleton to form a hair.},
  doi = {10.1016/S0955-0674(00)00263-5},
  file = {Adler01.pdf:biology/Adler01.pdf:PDF},
  institution = {Biology Department and Cancer Center, Gilmer Hall, University of
	Virginia, Charlottesville, Virginia 22903, USA. pna@virginia.edu},
  keywords = {Animals; Body Patterning; Cell Communication; Drosophila Proteins;
	Drosophila, embryology; Eye, embryology; Frizzled Receptors; Hair,
	embryology; Insect Proteins, physiology; Membrane Proteins, physiology;
	Models, Biological; Receptors, G-Protein-Coupled; Wing, embryology;
	PCP},
  language = {eng},
  medline-pst = {ppublish},
  owner = {barbierp},
  pii = {S0955-0674(00)00263-5},
  pmid = {11544034},
  timestamp = {2010.08.06}
}

@ARTICLE{Aida97,
  author = {Aida, M. and Ishida, T. and Fukaki, H. and Fujisawa, H. and Tasaka,
	M.},
  title = {Genes involved in organ separation in {{\itshape Arabidopsis}}: an
	analysis of the {{\itshape cup-shaped cotyledon}} mutant},
  journal = {Plant Cell},
  year = {1997},
  volume = {9},
  pages = {841--857},
  file = {:biology/Aida97.pdf:PDF}
}

@ARTICLE{Aida99,
  author = {Aida, M. and Ishida, T. and Tasaka, M.},
  title = {Shoot apical meristem and cotyledon formation during {A}rabidopsis
	embryogenesis: interaction among the {{\itshape CUP-SHAPED COTYLEDON}}
	and {{\itshape SHOOT MERISTEMLESS}} genes},
  journal = {Development},
  year = {1999},
  volume = {126},
  pages = {1563--1570},
  file = {:biology/Aida99.pdf:PDF}
}

@ARTICLE{Airy74,
  author = {Airy, Hubert},
  title = {On leaf-arrangement},
  journal = RSLBS,
  year = {1874},
  volume = {22},
  pages = {298--307},
  month = Apr,
  owner = {barbier}
}

@ARTICLE{Airy73,
  author = {Airy, Hubert},
  title = {On leaf-arrangement},
  journal = RSLBS,
  year = {1873},
  volume = {21},
  pages = {176--179},
  month = Feb,
  owner = {barbier}
}

@ARTICLE{Akberdin07,
  author = {Akberdin, Ilya R and Ozonov, Evgeniy A and Mironova, Victoria V and
	Omelyanchuk, Nadezda A and Likhoshvai, Vitaly A and Gorpinchenko,
	Dmytry N and Kolchanov, Nikolai A},
  title = {A cellular automaton to model the development of primary shoot meristems
	of Arabidopsis thaliana.},
  journal = JBCB,
  year = {2007},
  volume = {5},
  pages = {641--650},
  number = {2B},
  month = Apr,
  abstract = {Development of organisms is a very complex process in which a lot
	of gene networks of different cell types are integrated. Development
	of a cellular automaton (Ermentrout and Edelshtein-Keshet, J Theor
	Biol 160:97-133, 1993) that models the morphodynamics of different
	cell types is the first step in understanding and analysis of the
	regulatory mechanisms underlying the functioning of developmental
	gene networks. A model of a cellular automaton has been developed,
	which simulates the embryonic development of shoot meristem in Arabidopsis
	thaliana. The model adequately describes the basic stages in development
	of this organ in wild and mutant types.},
  doi = {10.1142/S0219720007002862},
  institution = {Institute of Cytology and Genetics SB RAS, Lavrentieva ave. 10 Novosibirsk,
	630090, Russia. akberdin@bionet.nsc.ru},
  keywords = {Arabidopsis Proteins, metabolism; Arabidopsis, physiology; Computer
	Simulation; Gene Expression Regulation, Developmental, physiology;
	Gene Expression Regulation, Plant, physiology; Meristem, physiology;
	Models, Biological; Morphogenesis, physiology; Plant Shoots, physiology;
	Signal Transduction, physiology},
  owner = {barbierp},
  pii = {S0219720007002862},
  pmid = {17636867},
  timestamp = {2008.12.08}
}

@ARTICLE{Akleman00,
  author = {Akleman, E and Cheng, Jin-Chen},
  title = {Guaranteeing the 2-manifold property for meshes with doubly linked
	face list},
  journal = IJSM,
  year = {2000},
  volume = {5},
  pages = {149--177},
  owner = {barbierp},
  timestamp = {2009.04.20}
}

@ARTICLE{Aloni03,
  author = {Aloni, Roni and Schwalm, Katja and Langhans, Markus and Ullrich,
	Cornelia I.},
  title = {Gradual shifts in sites of free-auxin production during leaf-primordium
	development and their role in vascular differentiation and leaf morphogenesis
	in {{\itshape Arabidopsis}}},
  journal = {Planta},
  year = {2003},
  volume = {216},
  pages = {841--853},
  number = {5},
  month = Mar,
  abstract = {The major regulatory shoot signal is auxin, whose synthesis in young
	leaves has been a mystery. To test the leaf-venation hypothesis [R.
	Aloni (2001) J Plant Growth Regul 20: 22-34], the patterns of free-auxin
	production, movement and accumulation in developing leaf primordia
	of DR5::GUS-transformed Arabidopsis thaliana (L.) Heynh. were visualized.
	DR5::GUS expression was regarded to reflect sites of free auxin,
	while immunolocalization with specific monoclonal antibodies indicated
	total auxin distribution. The mRNA expression of key enzymes involved
	in the synthesis, conjugate hydrolysis, accumulation and basipetal
	transport of auxin, namely indole-3-glycerol-phosphate-synthase,
	nitrilase, IAA-amino acid hydrolase, chalcone synthase and PIN1 as
	an essential component of the basipetal IAA carrier, was investigated
	by reverse transcription-polymerase chain reaction. Near the shoot
	apex, stipules were the earliest sites of high free-auxin production.
	During early stages of primordium development, leaf apical dominance
	was evident from strong beta-glucuronidase activity in the elongating
	tip, possibly suppressing the production of free auxin in the leaf
	tissues below it. Hydathodes, which develop in the tip and later
	in the lobes, were apparently primary sites of high free-auxin production,
	the latter supported by auxin-conjugate hydrolysis, auxin retention
	by the chalcone synthase-dependent action of flavonoids and also
	by the PIN1-component of the carrier-mediated basipetal transport.
	Trichomes and mesophyll cells were secondary sites of free-auxin
	production. During primordium development there are gradual shifts
	in sites and concentrations of free-auxin production occurring first
	in the tip of a leaf primordium, then progressing basipetally along
	the margins, and finally appearing also in the central regions of
	the lamina. This developmental pattern of free-auxin production is
	suggested to control the basipetal maturation sequence of leaf development
	and vascular differentiation in Arabidopsis leaves.},
  doi = {10.1007/s00425-002-0937-8},
  file = {:biology/Trichomes/Aloni03.pdf:PDF},
  keywords = {Acyltransferases, Amidohydrolases, Aminohydrolases, Arabidopsis, Bacterial
	Proteins, Biological Transport, Cell Differentiation, Cell Surface
	Extensions, Enzymologic, Gene Expression Regulation, Glucuronidase,
	Immunohistochemistry, Indole-3-Glycerol-Phosphate Synthase, Indoleacetic
	Acids, Morphogenesis, Non-U.S. Gov't, Peptidylprolyl Isomerase, Plant,
	Plant Leaves, Plant Roots, Plant Shoots, Research Support, 12624772,
	Trichome},
  owner = {barbier},
  pmid = {12624772},
  timestamp = {2006.03.13}
}

@ARTICLE{Amonlirdviman05,
  author = {Amonlirdviman, Keith and Khare, Narmada A and Tree, David R P and
	Chen, Wei-Shen and Axelrod, Jeffrey D and Tomlin, Claire J},
  title = {Mathematical modeling of planar cell polarity to understand domineering
	nonautonomy},
  journal = {Science},
  year = {2005},
  volume = {307},
  pages = {423--426},
  number = {5708},
  month = Jan,
  abstract = {Planar cell polarity (PCP) signaling generates subcellular asymmetry
	along an axis orthogonal to the epithelial apical-basal axis. Through
	a poorly understood mechanism, cell clones that have mutations in
	some PCP signaling components, including some, but not all, alleles
	of the receptor frizzled, cause polarity disruptions of neighboring
	wild-type cells, a phenomenon referred to as domineering nonautonomy.
	Here, a contact-dependent signaling hypothesis, derived from experimental
	results, is shown by reaction-diffusion, partial differential equation
	modeling and simulation to fully reproduce PCP phenotypes, including
	domineering nonautonomy, in the Drosophila wing. The sufficiency
	of this model and the experimental validation of model predictions
	reveal how specific protein-protein interactions produce autonomy
	or domineering nonautonomy.},
  doi = {10.1126/science.1105471},
  file = {Amonlirdviman05.pdf:bioinfo/Amonlirdviman05.pdf:PDF},
  institution = {Department of Aeronautics and Astronautics, Stanford University,
	Stanford, CA 94305-4035, USA.},
  keywords = {Adaptor Proteins, Signal Transducing; Alleles; Animals; Cell Membrane;
	Cell Polarity; Diffusion; Drosophila; Drosophila Proteins; Feedback,
	Biochemical; Frizzled Receptors; Mathematics; Membrane Proteins;
	Models, Biological; Mutation; Phenotype; Phosphoproteins; Protein
	Binding; Receptors, G-Protein-Coupled; Signal Transduction; Wing;
	PCP},
  owner = {barbierp},
  pii = {307/5708/423},
  pmid = {15662015},
  timestamp = {2008.10.23}
}

@ARTICLE{Ascher97,
  author = {Ascher, Uri M. and Ruuth, Steven J. and Spiteri, Raymond J.},
  title = {Implicit-explicit {Runge-Kutta} methods for time-dependent partial
	differential equations},
  journal = ANM,
  year = {1997},
  volume = {25},
  pages = {151--167},
  owner = {barbier},
  timestamp = {2007.12.19}
}

@ARTICLE{Audoly03,
  author = {B. Audoly and A. Boudaoud},
  title = {Self-similar structures near boundaries in strained systems.},
  journal = PRL,
  year = {2003},
  volume = {91},
  pages = {086105},
  number = {8},
  month = Aug,
  abstract = {We study the buckling of thin elastic plates caused by residual strains
	concentrated near a free edge. This is a model for plant leaves and
	torn plastic sheet morphologies. We derive new governing equations
	explaining self-similar patterns reported earlier in experiments.
	We reveal the cascade mechanism, determine the bounds for its wavelengths,
	and predict a similarity factor of 3 in agreement with experiments.
	This is confirmed by numerical solutions with up to five generations
	of wrinkles.},
  file = {Audoly03.pdf:math/Audoly03.pdf:PDF},
  institution = {Laboratoire de modélisation en mécanique, UMR 7607 du CNRS, Université
	Pierre et Marie Curie, 4 place Jussieu, F-75252 Paris Cedex 05, France.},
  owner = {barbierp},
  pmid = {14525264},
  timestamp = {2009.05.04}
}

@ARTICLE{Aurenhammer91,
  author = {Aurenhammer, Franz},
  title = {Voronoi diagrams: a survey of a fundamental geometric data structure},
  journal = CSurv,
  year = {1991},
  volume = {23},
  pages = {345--406},
  number = {3},
  month = Sep,
  abstract = {This paper presents a survey of the Voronoi diagram, one of the most
	fundamental data structures in computational geometry. It demonstrates
	the importance and usefulness of the Voronoi diagram in a wide variety
	of fields inside and outside computer science and surveys the history
	of its development. The paper puts particular emphasis on the unified
	exposition of its mathematical and algorithmic properties. Finally,
	the paper provides the first comprehensive bibliography on Voronoi
	diagrams and related structures.},
  doi = {10.1145/116873.116880},
  issn = {0360-0300}
}

@ARTICLE{Aurenhammer87,
  author = {Aurenhammer, Franz},
  title = {Power diagrams: properties, algorithms and applications},
  journal = SIAMJC,
  year = {1987},
  volume = {16},
  pages = {78--96},
  number = {1}
}

@ARTICLE{Avis81,
  author = {Avis, D. and Toussaint, G. T.},
  title = {An efficient algorithm for decomposing a polygon into star-shaped
	polygons},
  journal = PatRec,
  year = {1981},
  volume = {13},
  pages = {395--398},
  number = {6},
  month = May,
  doi = {doi:10.1016/0031-3203(81)90002-9},
  file = {Avis81.pdf:math/geometry/Avis81.pdf:PDF},
  owner = {barbierp},
  timestamp = {2009.09.30}
}

@ARTICLE{Avsian02,
  author = {Orna Avsian-Kretchmer and Jin-Chen Cheng and Lingjing Chen and Edga
	Moctezuma and Z. Renee Sung},
  title = {Indole acetic acid distribution coincides with vascular differenciation
	pattern during {A}rabidospsis leaf ontogeny},
  journal = PPh,
  year = {2002},
  volume = {130},
  pages = {199--209},
  month = Sep
}

@ARTICLE{Baines88,
  author = {M. J. Baines and A. J. Wathen},
  title = {Moving finite element methods for evolutionary problems. {I}. {T}heory},
  journal = JCP,
  year = {1988},
  volume = {79},
  pages = {245--269},
  number = {2},
  month = Dec,
  abstract = {In this paper, the first of two on the subject, we present a unified
	approach to moving and fixed finite element methods for evolutionary
	problems in terms of projections. The central theoretical results
	are concerned with moving finite elements for one-dimensional scalar
	problems (particularly hyperbolic equations with shocks), but the
	viewpoint extends to general systems in any number of dimensions.},
  doi = {10.1016/0021-9991(88)90016-2},
  owner = {barbier},
  timestamp = {2006.03.14}
}

@ARTICLE{Bansal06,
  author = {Mukesh Bansal and Giusy Della Gatta and Diego di Bernardo},
  title = {Inference of gene regulatory networks and compound mode of action
	from time course gene expression profiles.},
  journal = Bioinf,
  year = {2006},
  volume = {22},
  pages = {815--822},
  number = {7},
  month = Apr,
  abstract = {MOTIVATION: Time series expression experiments are an increasingly
	popular method for studying a wide range of biological systems. Here
	we developed an algorithm that can infer the local network of gene-gene
	interactions surrounding a gene of interest. This is achieved by
	a perturbation of the gene of interest and subsequently measuring
	the gene expression profiles at multiple time points. We applied
	this algorithm to computer simulated data and to experimental data
	on a nine gene network in Escherichia coli. RESULTS: In this paper
	we show that it is possible to recover the gene regulatory network
	from a time series data of gene expression following a perturbation
	to the cell. We show this both on simulated data and on a nine gene
	subnetwork part of the DNA-damage response pathway (SOS pathway)
	in the bacteria E. coli. CONTACT: dibernardo@tigem.it SUPPLEMENTARY
	INFORMATION: Supplementary data are available at http://dibernado.tigem.it.},
  doi = {10.1093/bioinformatics/btl003},
  file = {:bioinfo/Bansal06.pdf:PDF},
  keywords = {16418235},
  owner = {barbier},
  pii = {btl003},
  pmid = {16418235},
  timestamp = {2006.03.28}
}

@ARTICLE{Barber96,
  author = {C. Bradford Barber and David P. Dobkin and Hannu Huhdanpaa},
  title = {The quickhull algorithm for convex hulls},
  journal = ACMTMS,
  year = {1996},
  volume = {22},
  pages = {469--483},
  number = {4},
  month = Dec,
  abstract = {The convex hull of a set of points is the smallest convex set that
	contains the points. This paper presents a practical convex hull
	algorithm that combines the two-dimensional Quickhull Algorithm with
	the general dimension Beneath-Beyond Algorithm. It is similar to
	the randomized, incremental algorithms for convex hull and Delaunay
	triangulation. We provide empirical evidence that the algorithm runs
	faster when the input contains nonextreme points, and that it uses
	less memory. Computational geometry algorithms have traditionally
	assumed that input sets are well behaved. When an algorithm is implemented
	with floating point arithmetic, this assumption can lead to serious
	errors. We briefly describe a solution to this problem when computing
	the convex hull in two, three, or four dimensions. The output is
	a set of "thick" facets that contain all possible exact convex hulls
	of the input. A variation is effective in five or more dimensions.},
  bdsk-url-1 = {http://www.qhull.org/},
  bdsk-url-2 = {http://dx.doi.org/10.1145/235815.235821},
  bdsk-url-3 = {http://citeseer.ist.psu.edu/83502.html},
  citeseercitationcount = {0},
  citeseerurl = {http://citeseer.ist.psu.edu/83502.html},
  doi = {10.1145/235815.235821},
  file = {:prog/qhull/Barber96.pdf:PDF},
  issn = {0098-3500},
  url = {http://www.qhull.org/}
}

@PHDTHESIS{Barbier05a,
  author = {Barbier de Reuille, Pierre},
  title = {Vers un mod\`{e}le dynamique du merist\`{e}me apical caulinaire d'{{\em
	Arabidopsis thaliana}}.},
  school = {Universit\'{e}e de Montpellier II},
  year = {2005},
  month = Dec,
  abstract = {The huge quantity of data generated by the "large scale" biology allows
	for a new approach of developmental biology : an approach based on
	modeling at a cellular level. Nowadays, genetic patterns and genetics
	pathways involved in morphogenesis begin to be analyzable. In that
	context, it becomes possible to understand how the plants architecture
	may be influenced by these cellular or molecular scale mechanisms.
	
	In a first part of this work, tools dedicated to digitization and
	analysis of cellular tissues and their evolution through time were
	developed. We set up a software chain for quantitative analysis of
	morphological characteristics of plant tissues through time, starting
	from images created using an acquisition protocol based on confocal
	microscopy.
	
	Then, we developed a first growth model of the shoot apical meristem
	(a population of stem cells in the plants) to study the initiation
	of lateral organs. To account for existing biological knowledge,
	our model was developed at organ scale. The genetic state, the physiological
	state and the growth of each cell are simulated together with hormones
	fluxes between cells. This model allowed for prediction and analysis
	of accumulation zones of hormones in digitized meristems. Thanks
	to these studies, we were able to develop a dynamic model of the
	meristem from which phyllotactic patterns emerge from cell growth
	and cell-cell interactions.
	
	All the computer tools developed during this PhD have been integrated
	into a multi-language software platform. In particular, this platform
	was used to test different software development techniques involved
	in the integration of compiled and interpreted languages in the context
	of morphogenesis study.},
  file = {:these_full.pdf:PDF},
  keywords = {auxin, transport model, dynamic systems, 3D reconstruction, imaging,
	sofware platform, cell lineage, phyllotaxis},
  owner = {barbier},
  timestamp = {2006.09.04}
}

@ARTICLE{Barbier05,
  author = {Barbier de Reuille, Pierre and Bohn-Courseau, Isabelle and Godin,
	Christophe and Traas, Jan},
  title = {A protocol to analyse cellular dynamics during plant development},
  journal = TPJ,
  year = {2005},
  volume = {44},
  pages = {1045--1053},
  number = {6},
  month = Dec,
  abstract = {In vivo microscopy generates images that contain complex information
	on the dynamic behaviour of three-dimensional (3D) objects. As a
	result, adapted mathematical and computational tools are required
	to help in their interpretation. Ideally, a complete software chain
	to study the dynamics of a complex 3D object should include: (i)
	the acquisition, (ii) the preprocessing and (iii) segmentation of
	the images, followed by (iv) a reconstruction in time and space and
	(v) the final quantitative analysis. Here, we have developed such
	a protocol to study cell dynamics at the shoot apical meristem in
	Arabidopsis. The protocol uses serial optical sections made with
	the confocal microscope. It includes specially designed algorithms
	to automate the identification of cell lineage and to analyse the
	quantitative behaviour of the meristem surface.},
  doi = {10.1111/j.1365-313X.2005.02576.x},
  file = {:biology/cell/Barbier05_full.pdf:PDF},
  keywords = {confocal microscopy, image analysis, cell lineage, shoot apical meristem},
  owner = {barbier},
  timestamp = {2006.01.03}
}

@ARTICLE{Reuille06,
  author = {Barbier de Reuille, Pierre and Isabelle Bohn-Courseau and Karin Ljung
	and Halima Morin and Nicola Carraro and Christophe Godin and Jan
	Traas},
  title = {Computer simulations reveal properties of the cell-cell signaling
	network at the shoot apex in {A}rabidopsis.},
  journal = PNAS,
  year = {2006},
  volume = {103},
  pages = {1627--1632},
  number = {5},
  month = Jan,
  abstract = {The active transport of the plant hormone auxin plays a major role
	in the initiation of organs at the shoot apex. Polar localized membrane
	proteins of the PIN1 family facilitate this transport, and recent
	observations suggest that auxin maxima created by these proteins
	are at the basis of organ initiation. This hypothesis is based on
	the visual, qualitative characterization of the complex distribution
	patterns of the PIN1 protein in Arabidopsis. To take these analyses
	further, we investigated the properties of the patterns using computational
	modeling. The simulations reveal previously undescribed properties
	of PIN1 distribution. In particular, they suggest an important role
	for the meristem summit in the distribution of auxin. We confirm
	these predictions by further experimentation and propose a detailed
	model for the dynamics of auxin fluxes at the shoot apex.},
  doi = {10.1073/pnas.0510130103},
  file = {:bioinfo/Reuille06.pdf:PDF},
  keywords = {auxin, modeling, shoot meristem, 16432202},
  owner = {barbier},
  pii = {0510130103},
  pmid = {16432202},
  timestamp = {2006.03.15}
}

@ARTICLE{Bard81,
  author = {J. B. Bard},
  title = {A model for generating aspects of zebra and other mammalian coat
	patterns},
  journal = JTB,
  year = {1981},
  volume = {93},
  pages = {363--385},
  number = {2},
  month = Nov,
  abstract = {A model is put forward which is capable of generating chemical maps
	whose concentration contours are similar to the patterns seen on
	the flanks of zebras, cats and other mammals. The model derives from
	the reaction-diffusion kinetics invented by Turing (1952) and it
	is assumed that the necessary molecular apparatus is present in each
	cell of a two-dimensional array and that the cells are in diffusion
	contact. The model was expressed in differential equation form and
	solved digitally under a range of different initial, boundary and
	other conditions. The main forms of pattern that the model generated
	were spots of variable complexity, rings, and both vertical and horizontal
	stripes. If morphogen concentration levels are assumed to act as
	melanin-production switches, then a common basic mechanism is capable
	of generating a variety of skin patterns. Simple spots such as those
	found in the fallow deer or the serval, F. serval, are generated
	if the kinetics are initiated simultaneously in each cell and interpretation
	depends only on the presence or absence of morphogen, which is assumed
	for the deer to be an activator and for the cat a suppressor of pigment
	formation. The reticulated pattern of the giraffe is generated if
	there is a single high-value threshold. Complex spots typical of
	the leopards can be produced if there are different concentration
	thresholds for different colours. Rings of pattern typical of those
	found on cat tails are generated if the cellular array is a very
	narrow cylinder. Horizontal stripes are generated if the kinetics
	in each cell are initiated by a diffusion gradient whose source is
	the dorsal line of cells and these stripes may break up into spots
	to give a pattern very similar to that of, for example, the fishing
	cat, F. viverina. The vertical stripes of the caffre cat, F. caffra,
	or the zebras are formed if the kinetics are initiated by a vertically-moving
	constant-velocity wave which also allows morphogen diffusion between
	previously uncoupled cells. Thus far, the mechanism has generated
	neither the triradii that are commonly found on forelimbs nor the
	rings often observed on mammalian limbs. It does however incorporate
	the randomness that characterizes skin pattern, its operation is
	of the scale required in embryogenesis, it can be made stable to
	growth and it can explain certain degenerate patterns. Analysis of
	a spotted zebra in the light of the model provides evidence that
	zebra stripes arise from the inhibition rather than the stimulation
	of melanin; their pattern is thus of white stripes on a black background.},
  doi = {10.1016/0022-5193(81)90109-0},
  file = {:math/reaction-diffusion/Bard81.pdf:PDF},
  keywords = {Animals; Artiodactyla; Carnivora; Cats; Computers; Diffusion; Hair
	Color; Kinetics; Models, Biological; Perissodactyla; Skin},
  owner = {barbier},
  pii = {0022-5193(81)90109-0},
  pmid = {7334825},
  timestamp = {2007.02.21}
}

@ARTICLE{Bartel97,
  author = {Bonnie Bartel},
  title = {A{UXIN} {BIOSYNTHESIS}},
  journal = ARPPPMB,
  year = {1997},
  volume = {48},
  pages = {51--66},
  month = Jun,
  abstract = {Indole-3-acetic acid (IAA) is the most abundant naturally occurring
	auxin. Plants produce active IAA both by de novo synthesis and by
	releasing IAA from conjugates. This review emphasizes recent genetic
	experiments and complementary biochemical analyses that are beginning
	to unravel the complexities of IAA biosynthesis in plants. Multiple
	pathways exist for de novo IAA synthesis in plants, and a number
	of plant enzymes can liberate IAA from conjugates. This multiplicity
	has contributed to the current situation in which no pathway of IAA
	biosynthesis in plants has been unequivocally established. Genetic
	and biochemical experiments have demonstrated both tryptophan-dependent
	and tryptophan-independent routes of IAA biosynthesis. The recent
	application of precise and sensitive methods for quantitation of
	IAA and its metabolites to plant mutants disrupted in various aspects
	of IAA regulation is beginning to elucidate the multiple pathways
	that control IAA levels in the plant.},
  doi = {10.1146/annurev.arplant.48.1.51},
  keywords = {15012256},
  pmid = {15012256}
}

@ARTICLE{Barton93,
  author = {Barton, M.K. and Poethig, R.S.},
  title = {Formation of the shoot apical meristem in {{itshape Arabidopsis thaliana}}:
	an analysis of development in the wild-type and in the {\itshape
	shoot meristemless} mutant},
  journal = {Development},
  year = {1993},
  volume = {119},
  pages = {823--831},
  number = {3},
  month = Nov,
  abstract = {The primary shoot apical meristem of Arabidopsis is initiated late
	in embryogenesis, after the initiation of the cotyledons. We have
	identified a gene, called SHOOT MERISTEMLESS, which is critical for
	this process. shoot meristemless mutant seedlings lack a shoot apical
	meristem but are otherwise healthy and viable. The anatomy of mutant
	embryos demonstrates that the shoot meristemless-1 mutation completely
	blocks the initiation of the shoot apical meristem, but has no other
	obvious effects on embryo development. The failure of shoot meristemless
	tissue to regenerate shoots in tissue culture suggests that this
	gene regulates adventitious shoot meristem formation, as well as
	embryonic shoot meristem formation.},
  file = {:biology/Barton93.pdf:PDF},
  keywords = {meristem, SHOOT MERISTEMLESS, plant development, Arabidopsis, embryogenesis}
}

@ARTICLE{Bassingthwaighte06,
  author = {Bassingthwaighte, James B. and Chizeck, Howard Jay and Atlas, Les
	E.},
  title = {Strategies and tactics in multiscale modeling of cell-to-organ systems},
  journal = PIEEE,
  year = {2006},
  volume = {94},
  pages = {819--831},
  number = {4},
  month = Apr,
  abstract = {Modeling is essential to integrating knowledge of human physiology.
	Comprehensive self-consistent descriptions expressed in quantitative
	mathematical form define working hypotheses in testable and reproducible
	form, and though such models are always "wrong" in the sense of being
	incomplete or partly incorrect, they provide a means of understanding
	a system and improving that understanding. Physiological systems,
	and models of them, encompass different levels of complexity. The
	lowest levels concern gene signaling and the regulation of transcription
	and translation, then biophysical and biochemical events at the protein
	level, and extend through the levels of cells, tissues and organs
	all the way to descriptions of integrated systems behavior. The highest
	levels of organization represent the dynamically varying interactions
	of billions of cells. Models of such systems are necessarily simplified
	to minimize computation and to emphasize the key factors defining
	system behavior; different model forms are thus often used to represent
	a system in different ways. Each simplification of lower level complicated
	function reduces the range of accurate operability at the higher
	level model, reducing robustness, the ability to respond correctly
	to dynamic changes in conditions. When conditions change so that
	the complexity reduction has resulted in the solution departing from
	the range of validity, detecting the deviation is critical, and requires
	special methods to enforce adapting the model formulation to alternative
	reduced-form modules or decomposing the reduced-form aggregates to
	the more detailed lower level modules to maintain appropriate behavior.
	The processes of error recognition, and of mapping between different
	levels of model complexity and shifting the levels of complexity
	of models in response to changing conditions, are essential for adaptive
	modeling and computer simulation of large-scale systems in reasonable
	time.},
  doi = {10.1109/JPROC.2006.871775},
  file = {:bioinfo/Bassingthwaighte06.pdf:PDF},
  keywords = {Adaptive model configuration, cardiac contraction, cardiac metabolic
	systems modeling, constraint-based analysis, data analysis, energetics,
	model aggregation, multicellular tissues, multiscale, optimization,
	oxidative phosphorylation},
  owner = {pbarbier},
  timestamp = {2007.05.14}
}

@ARTICLE{Bayer09,
  author = {Emmanuelle M Bayer and Richard S Smith and Therese Mandel and Naomi
	Nakayama and Michael Sauer and Przemyslaw Prusinkiewicz and Cris
	Kuhlemeier},
  title = {Integration of transport-based models for phyllotaxis and midvein
	formation.},
  journal = GDev,
  year = {2009},
  volume = {23},
  pages = {373--384},
  number = {3},
  month = Feb,
  __markedentry = {[barbierp]},
  abstract = {The plant hormone auxin mediates developmental patterning by a mechanism
	that is based on active transport. In the shoot apical meristem,
	auxin gradients are thought to be set up through a feedback loop
	between auxin and the activity and polar localization of its transporter,
	the PIN1 protein. Two distinct molecular mechanisms for the subcellular
	polarization of PIN1 have been proposed. For leaf positioning (phyllotaxis),
	an "up-the-gradient" PIN1 polarization mechanism has been proposed,
	whereas the formation of vascular strands is thought to proceed by
	"with-the-flux" PIN1 polarization. These patterning mechanisms intersect
	during the initiation of the midvein, which raises the question of
	how two different PIN1 polarization mechanisms may work together.
	Our detailed analysis of PIN1 polarization during midvein initiation
	suggests that both mechanisms for PIN1 polarization operate simultaneously.
	Computer simulations of the resulting dual polarization model are
	able to reproduce the dynamics of observed PIN1 localization. In
	addition, the appearance of high auxin concentration in our simulations
	throughout the initiation of the midvein is consistent with experimental
	observation and offers an explanation for a long-standing criticism
	of the canalization hypothesis; namely, how both high flux and high
	concentration can occur simultaneously in emerging veins.},
  doi = {10.1101/gad.497009},
  file = {Bayer09.pdf:bioinfo/Bayer09.pdf:PDF},
  institution = {Institute of Plant Sciences, University of Bern, Bern, Switzerland.},
  keywords = {Base Sequence; Biological Transport, Active; Body Patterning, drug
	effects; Computer Simulation; DNA Primers, genetics; DNA, Plant,
	genetics; Feedback, Physiological; Gene Expression Regulation, Developmental;
	Gene Expression Regulation, Plant; Genes, Plant; Indoleacetic Acids,
	metabolism/pharmacology; Lycopersicon esculentum, drug effects/genetics/growth
	/&/ development/physiology; Meristem, growth /&/ development/physiology;
	Models, Biological; Plant Growth Regulators, pharmacology/physiology;
	Plant Leaves, growth /&/ development/physiology; Plant Proteins,
	genetics/physiology; Plants, Genetically Modified},
  language = {eng},
  medline-pst = {ppublish},
  owner = {barbierp},
  pii = {23/3/373},
  pmid = {19204121},
  timestamp = {2011.01.18}
}

@ARTICLE{Benjamins01,
  author = {R. Benjamins and A. Quint and D. Weijers and P. Hooykaas and R. Offringa},
  title = {The {PINOID} protein kinase regulates organ development in {{\itshape
	Arabidopsis}} by enhancing polar auxin transport},
  journal = {Development},
  year = {2001},
  volume = {128},
  pages = {4057--4067},
  number = {20},
  month = Oct,
  abstract = {Arabidopsis pinoid mutants show a strong phenotypic resemblance to
	the pin-formed mutant that is disrupted in polar auxin transport.
	The PINOID gene was recently cloned and found to encode a protein-serine/threonine
	kinase. Here we show that the PINOID gene is inducible by auxin and
	that the protein kinase is present in the primordia of cotyledons,
	leaves and floral organs and in vascular tissue in developing organs
	or proximal to meristems. Overexpression of PINOID under the control
	of the constitutive CaMV 35S promoter (35S::PID) resulted in phenotypes
	also observed in mutants with altered sensitivity to or transport
	of auxin. A remarkable characteristic of high expressing 35S::PID
	seedlings was a frequent collapse of the primary root meristem. This
	event triggered lateral root formation, a process that was initially
	inhibited in these seedlings. Both meristem organisation and growth
	of the primary root were rescued when seedlings were grown in the
	presence of polar auxin transport inhibitors, such as naphthylphtalamic
	acid (NPA). Moreover, ectopic expression of PINOID cDNA under control
	of the epidermis-specific LTP1 promoter provided further evidence
	for the NPA-sensitive action of PINOID. The results presented here
	indicate that PINOID functions as a positive regulator of polar auxin
	transport. We propose that PINOID is involved in the fine-tuning
	of polar auxin transport during organ formation in response to local
	auxin concentrations.},
  file = {:biology/Benjamins01.pdf:PDF},
  keywords = {8-Bromo Cyclic Adenosine Monophosphate, Active, Animals, Apoptosis,
	Arabidopsis, Arabidopsis Proteins, Auxins, Base Sequence, Biological,
	Biological Transport, Caspases, Cell Differentiation, Cell Line,
	Cell Nucleus, Cells, Central Nervous System, Comparative Study, Complementary,
	Cultured, Cyclic AMP, Cytokines, DNA, DNA Fragmentation, Demyelinating
	Diseases, Developmental, Dose-Response Relationship, Down-Regulation,
	Drug, Dyes, Enzyme Inhibitors, Enzymologic, Galactolipids, Gene Expression
	Regulation, Genes, Glycolipids, Humans, In, Inflammation, Models,
	Multiple Sclerosis, Mutation, Necrosis, Nerve Growth Factor, Newborn,
	Non-U.S. Gov't, Oligodendroglia, P.H.S., Peripheral Nervous System,
	Phenotype, Plant, Propidium, Protein-Serine-Threonine Kinases, Rats,
	Receptor, Research Support, Schwann Cells, Signal Transduction, Single-Stranded,
	Sprague-Dawley, Staurosporine, Temperature, Transformed, Transforming
	Growth Factor beta, Trypan Blue, Tumor Necrosis Factor-alpha, U.S.
	Gov't, Up-Regulation, terferon Type II, 11641228},
  pmid = {11641228}
}

@ARTICLE{Benkova03,
  author = {Benkova, E. and Michniewicz, M. and Sauer, M. and Teichmann, T. and
	Seifertova, D. and Jurgens, G. and Friml, J.},
  title = {Local, efflux-dependent auxin gradients as a common module for plant
	organ formation},
  journal = {Cell},
  year = {2003},
  volume = {115},
  pages = {591--602},
  file = {:biology/Benkova03.pdf:PDF}
}

@ARTICLE{Bennett96,
  author = {Bennett, Malcom J. and Marchant, A. and Green, H. G. and May, S.
	T. and Ward, S. P. and Millner, P. A. and Walker, A. R. and Schulz,
	B. and Feldmann, K. A.},
  title = {Arabidopsis {{\itshape AUX1}} gene: a permease-like regulator of
	root gravitropism},
  journal = {Science},
  year = {1996},
  volume = {273},
  pages = {948--950},
  number = {5277},
  month = Aug,
  keywords = {2,4-Dichlorophenoxyacetic Acid, Amino Acid Sequence, Amino Acid Transport
	Systems, Amino Acids, Arabidopsis, Arabidopsis Proteins, Auxins,
	Bacterial, Biological Transport, Cloning, DNA, Genes, Genetic Complementation
	Test, Gravitropism, Indoleacetic Acids, Membrane Transport Proteins,
	Molecular, Molecular Sequence Data, Molecular Weight, Mutation, Non-U.S.
	Gov't, Plant, Plant Proteins, Plant Roots, Research Support, Sequence
	Alignment, Signal Transduction, 8688077}
}

@ARTICLE{Bennett95,
  author = {Bennett, Sally R.M. and Alvarez, John and Bossinger, Gerd and Smyth,
	David R.},
  title = {Morphogenesis in {{\itshape pinoid}} mutants of {{\itshape Arabidopsis
	thaliana}}},
  journal = TPJ,
  year = {1995},
  volume = {8},
  pages = {505--520},
  number = {4},
  month = Oct,
  abstract = {A series of mutants of Arabidopsis thaliana was selected in which
	the inflorescence stem elongates but loses the ability to produce
	flower primordia on its flanks. Mutants fell into two classes, further
	occurrences of pin-formed mutants and mutations at a new locus named
	pinoid. As well as causing inflorescence defects, pinoid mutations
	result in pleiotropic defects in the development of floral organs,
	cotyledons and leaves. Most changes involve the number of organs
	produced rather than their differentiation suggesting that PINOID
	controls an early general step in meristem development. pinoid mutant
	defects are similar to those seen in pin-formed mutants for inflorescences
	and flowers, but different for cotyledons and leaves indicating that
	the two genes have separate but overlapping functions. A defect in
	polar auxin transport is implicated in the pin-formed mutant phenotype,
	but in young inflorescence stems of even the strongest pinoid mutants
	it occurs at close to wild-type levels. It is markedly reduced only
	after stems have ceased elongating. Thus, it is likely that polar
	auxin transport is secondarily affected in pinoid mutants rather
	than being directly controlled by the PINOID gene product. Even so,
	double mutant studies indicate that the process controlled by PINOID
	overlaps with that specified by the AUXIN RESISTANT1 gene, suggesting
	that PINOID plays some role in an auxin-related process.},
  doi = {10.1046/j.1365-313X.1995.8040505.x},
  file = {:biology/Bennett95.pdf:PDF},
  owner = {barbier}
}

@ARTICLE{deBerg98,
  author = {de Berg, Mark and Dobrindt, Katrin T. G.},
  title = {On levels of detail in terrains},
  journal = GMIP,
  year = {1998},
  volume = {60},
  pages = {1--12},
  number = {1},
  month = Jan
}

@ARTICLE{Bergdorf10,
  author = {Michael Bergdorf and Ivo F Sbalzarini and Petros Koumoutsakos},
  title = {A Lagrangian particle method for reaction-diffusion systems on deforming
	surfaces.},
  journal = JMB,
  year = {2010},
  volume = {61},
  pages = {649--663},
  number = {5},
  month = Nov,
  abstract = {Reaction-diffusion processes on complex deforming surfaces are fundamental
	to a number of biological processes ranging from embryonic development
	to cancer tumor growth and angiogenesis. The simulation of these
	processes using continuum reaction-diffusion models requires computational
	methods capable of accurately tracking the geometric deformations
	and discretizing on them the governing equations. We employ a Lagrangian
	level-set formulation to capture the deformation of the geometry
	and use an embedding formulation and an adaptive particle method
	to discretize both the level-set equations and the corresponding
	reaction-diffusion. We validate the proposed method and discuss its
	advantages and drawbacks through simulations of reaction-diffusion
	equations on complex and deforming geometries.},
  doi = {10.1007/s00285-009-0315-2},
  file = {Bergdorf10.pdf:bioinfo/Bergdorf10.pdf:PDF},
  institution = {Department of Computational Science, ETH Zurich, Zurich, Switzerland.},
  language = {eng},
  medline-pst = {ppublish},
  owner = {barbierp},
  pmid = {20020130},
  timestamp = {2010.11.10}
}

@ARTICLE{Berleth07,
  author = {Thomas Berleth and Enrico Scarpella and Przemys\l{}aw Prusinkiewicz},
  title = {Towards the systems biology of auxin-transport-mediated patterning.},
  journal = {Trends Plant Sci},
  year = {2007},
  volume = {12},
  pages = {151--159},
  number = {4},
  month = {Apr},
  abstract = {Polar auxin transport intimately connects plant cell polarity and
	multicellular patterning. Through the transport of the small molecule
	indole-3-acetic acid, plant cells integrate their polarities and
	communicate the degree of their polarization. In this way, they generate
	an apical-basal axis that serves as a positional reference anchoring
	subsequent patterning events. Research in recent years has brought
	the molecular mechanisms underlying auxin perception and auxin transport
	to light. This knowledge has been used to derive spectacular molecular
	visualization tools and animated computer simulations, which are
	now allied in a joint systems biology effort towards a mathematical
	description of auxin-transport-mediated patterning processes.},
  doi = {10.1016/j.tplants.2007.03.005},
  file = {:bioinfo/Berleth07.pdf:PDF},
  institution = {Department of Cell and Systems Biology, University of Toronto, 25
	Willcocks Street, Toronto ON, M5S 3B2, Canada. thomas.berleth@utoronto.ca},
  keywords = {Biological Transport; Body Patterning; Cell Polarity; Computer Simulation;
	Indoleacetic Acids; Meristem; Models, Biological; Plants; Systems
	Biology},
  owner = {pbarbier},
  pii = {S1360-1385(07)00061-1},
  pmid = {17368963},
  timestamp = {2007.09.25}
}

@ARTICLE{Bernhardt03,
  author = {Christine Bernhardt and Myeong Min Lee and Antonio Gonzalez and Fan
	Zhang and Alan Lloyd and John Schiefelbein},
  title = {The bHLH genes GLABRA3 (GL3) and ENHANCER OF GLABRA3 (EGL3) specify
	epidermal cell fate in the Arabidopsis root.},
  journal = {Development},
  year = {2003},
  volume = {130},
  pages = {6431--6439},
  number = {26},
  month = Dec,
  abstract = {The position-dependent specification of the hair and non-hair cell
	types in the Arabidopsis root epidermis provides a simple model for
	the study of cell fate determination in plants. Several putative
	transcriptional regulators are known to influence this cell fate
	decision. Indirect evidence from studies with the maize R gene has
	been used to suggest that a bHLH transcription factor also participates
	in this process. We show that two Arabidopsis genes encoding bHLH
	proteins, GLABRA3 (GL3) and ENHANCER OF GLABRA3 (EGL3), act in a
	partially redundant manner to specify root epidermal cell fates.
	Plants homozygous for mutations in both genes fail to specify the
	non-hair cell type, whereas plants overexpressing either gene produce
	ectopic non-hair cells. We also find that these genes are required
	for appropriate transcription of the non-hair specification gene
	GL2 and the hair cell specification gene CPC, showing that GL3 and
	EGL3 influence both epidermal cell fates. Furthermore, we show that
	these bHLH proteins require a functional WER MYB protein for their
	action, and they physically interact with WER and CPC in the yeast
	two-hybrid assay. These results suggest a model in which GL3 and
	EGL3 act together with WER in the N cell position to promote the
	non-hair cell fate, whereas they interact with the incomplete MYB
	protein CPC in the H position, which blocks the non-hair pathway
	and leads to the hair cell fate.},
  doi = {10.1242/dev.00880},
  file = {:biology/Trichomes/Bernhardt03.pdf:PDF},
  keywords = {Arabidopsis; Arabidopsis Proteins; Basic Helix-Loop-Helix Transcription
	Factors; Carrier Proteins; Gene Expression Regulation, Developmental;
	Gene Expression Regulation, Plant; Helix-Loop-Helix Motifs; Plant
	Roots; Plants, Genetically Modified; RNA, Plant; Transcription Factors;
	Transcription, Genetic},
  owner = {pbarbier},
  pii = {dev.00880},
  pmid = {14627722},
  timestamp = {2007.02.07}
}

@ARTICLE{Bernhardt05,
  author = {Christine Bernhardt and Mingzhe Zhao and Antonio Gonzalez and Alan
	Lloyd and John Schiefelbein},
  title = {The bHLH genes GL3 and EGL3 participate in an intercellular regulatory
	circuit that controls cell patterning in the Arabidopsis root epidermis.},
  journal = {Development},
  year = {2005},
  volume = {132},
  pages = {291--298},
  number = {2},
  month = Jan,
  abstract = {The specification of the hair and non-hair cells in the Arabidopsis
	root epidermis provides a useful model for the study of cell fate
	determination in plants. A network of putative transcriptional regulators,
	including the related bHLH proteins GLABRA3 (GL3) and ENHANCER OF
	GLABRA3 (EGL3), is known to influence the patterning of these cell
	types. Here, we analyze the expression and regulation of GL3 and
	EGL3 during root epidermis development. Although they are thought
	to act in both the hair and non-hair cell types, we surprisingly
	found that GL3 and EGL3 gene expression and RNA accumulation occurs
	preferentially in the developing hair cells. By analyzing the expression
	of GL3::GUS and EGL3::GUS reporter fusions in various mutant and
	overexpression lines, we discovered that the expression of both genes
	is negatively regulated by WER, GL3 and EGL3 in the developing non-hair
	cells, and positively regulated by the CPC and TRY proteins in the
	developing hair cells. Further, the analysis of a GL3-YFP translational
	fusion, expressed under the GL3 promoter, indicates that the GL3
	protein moves from the hair cells to the non-hair cells. These results
	suggest that GL3/EGL3 accumulation in the N cells is dependent on
	specification of the hair cell fate, which itself is known to be
	influenced (via CPC-mediated lateral inhibition) by the non-hair
	cells. This bi-directional signaling mechanism defines a new regulatory
	circuit of intercellular communication to specify the epidermal cell
	types.},
  doi = {10.1242/dev.01565},
  file = {:biology/Trichomes/Bernhardt05.pdf:PDF},
  keywords = {Alleles; Arabidopsis; Arabidopsis Proteins; Basic Helix-Loop-Helix
	Transcription Factors; Carrier Proteins; Cell Communication; Cell
	Differentiation; Gene Expression Regulation, Developmental; Hair
	Cells; In Situ Hybridization; Models, Biological; Models, Genetic;
	Mutation; Plant Roots; Promoter Regions (Genetics); Protein Biosynthesis;
	RNA; RNA, Messenger; Recombinant Fusion Proteins; Signal Transduction},
  owner = {pbarbier},
  pii = {dev.01565},
  pmid = {15590742},
  timestamp = {2007.02.07}
}

@ARTICLE{Bessonov08,
  author = {N. Bessonov and N. Morozova and V. Volpert},
  title = {Modeling of branching patterns in plants.},
  journal = {Bull Math Biol},
  year = {2008},
  volume = {70},
  pages = {868--893},
  number = {3},
  month = {Apr},
  abstract = {A major determinant of plant architecture is the arrangement of branches
	around the stem, known as phyllotaxis. However, the specific form
	of branching conditions is not known. Here we discuss this question
	and suggest a branching model which seems to be in agreement with
	biological observations.Recently, a number of models connected with
	the genetic network or molecular biology regulation of the processes
	of pattern formation appeared. Most of these models consider the
	plant hormone, auxin, transport and distribution in the apical meristem
	as the main factors for pattern formation and phyllotaxis. However,
	all these models do not take into consideration the whole plant morphogenesis,
	concentrating on the events in the shoot or root apex. On the other
	hand, other approaches for modeling phyllotaxis, where the whole
	plant is considered, usually are mostly phenomenological, and due
	to it, do not describe the details of plant growth and branching
	mechanism.In this work, we develop a mathematical model and study
	pattern formation of the whole, though simplified, plant organism
	where the main physiological factors of plant growth and development
	are taken into consideration. We model a growing plant as a system
	of intervals, which we will consider as branches. We assume that
	the number and location of the branches are not given a priori, but
	appear and grow according to certain rules, elucidated by the application
	of mathematical modeling.Four variables are included in our model:
	concentrations of the plant hormones auxin and cytokinin, proliferation
	and growth factor, and nutrients-we observe a wide variety of plant
	forms and study more specifically the involvement of each variable
	in the branching process. Analysis of the numerical simulations shows
	that the process of pattern formation in plants depends on the interaction
	of all these variables. While concentrations of auxin and cytokinin
	determine the appearance of a new bud, its growth is determined by
	the concentrations of nutrients and proliferation factors. Possible
	mechanisms of apical domination in the frame of our model are discussed.},
  doi = {10.1007/s11538-007-9282-1},
  institution = {Institute of Mechanical Engineering Problems, 199178, Saint Petersburg,
	Russia.},
  keywords = {Computer Simulation; Models, Biological; Morphogenesis; Plant Shoots,
	growth /&/ development; Plants, growth /&/ development},
  owner = {barbierp},
  pmid = {18266043},
  timestamp = {2008.12.08},
  url = {http://dx.doi.org/10.1007/s11538-007-9282-1}
}

@INPROCEEDINGS{Biermann00,
  author = {Biermann, Henning and Levin, Adi and Zorin, Denis},
  title = {Piecewise smooth subdivision surfaces with normal control},
  booktitle = {Proceedings of the 27th Annual Conference on Computer Graphics and
	Interactive Techniques},
  year = {2000},
  abstract = {In this paper we introduce improved rules for Catmull-Clark and Loop
	subdivision that overcome several problems with the original schemes
	(lack of smoothness at extraordinary boundary vertices, folds near
	concave corners). In addition, our approach to rule modification
	allows generation of surfaces with prescribed normals, both on the
	boundary and in the interior, which considerably improves control
	of the shape of surfaces.},
  file = {:prog/geometry/Biermann00.pdf:PDF},
  owner = {pbarbier},
  timestamp = {2007.09.26}
}

@INPROCEEDINGS{Blake04,
  author = {A. Blake and C. Rother and M. Brown and P. Perez and P. Torr},
  title = {Interactive image segmentation using an adaptive {GMMRF} model.},
  booktitle = {Proceedings European Conference Computer Vision},
  year = {2004},
  file = {:math/image/Blake04.pdf:PDF},
  owner = {barbier},
  timestamp = {2006.05.18}
}

@ARTICLE{Blilou05,
  author = {Ikram Blilou and Jian Xu and Marjolein Wildwater and Viola Willemsen
	and Ivan Paponov and Jir{\'i} Friml and Renze Heidstra and Mitsuhiro
	Aida and Klaus Palme and Ben Scheres},
  title = {The PIN auxin efflux facilitator network controls growth and patterning
	in Arabidopsis roots.},
  journal = {Nature},
  year = {2005},
  volume = {433},
  pages = {39--44},
  number = {7021},
  month = {Jan},
  abstract = {Local accumulation of the plant growth regulator auxin mediates pattern
	formation in Arabidopsis roots and influences outgrowth and development
	of lateral root- and shoot-derived primordia. However, it has remained
	unclear how auxin can simultaneously regulate patterning and organ
	outgrowth and how its distribution is stabilized in a primordium-specific
	manner. Here we show that five PIN genes collectively control auxin
	distribution to regulate cell division and cell expansion in the
	primary root. Furthermore, the joint action of these genes has an
	important role in pattern formation by focusing the auxin maximum
	and restricting the expression domain of PLETHORA (PLT) genes, major
	determinants for root stem cell specification. In turn, PLT genes
	are required for PIN gene transcription to stabilize the auxin maximum
	at the distal root tip. Our data reveal an interaction network of
	auxin transport facilitators and root fate determinants that control
	patterning and growth of the root primordium.},
  doi = {10.1038/nature03184},
  institution = {Department of Molecular Genetics, Utrecht University, Padualaan 8,
	3584CH Utrecht, The Netherlands.},
  keywords = {Arabidopsis Proteins, genetics/metabolism; Arabidopsis, cytology/embryology/genetics/metabolism;
	Body Patterning; Cell Division; Cell Enlargement; Gene Expression
	Regulation, Plant; Genes, Plant, genetics/physiology; Indoleacetic
	Acids, metabolism; Membrane Transport Proteins, genetics/metabolism;
	Meristem, cytology/genetics/metabolism; Models, Biological; Mutation,
	genetics; Plant Roots, cytology/embryology/genetics/metabolism; Protein
	Transport; RNA Transport; RNA, Messenger, genetics/metabolism; Transcription
	Factors, genetics/metabolism},
  owner = {barbierp},
  pii = {nature03184},
  pmid = {15635403},
  timestamp = {2008.12.08}
}

@INBOOK{Boas83,
  chapter = {Ordinary differential equations},
  pages = {337--381},
  title = {Methematical methods in the physical sciences},
  publisher = {Wiley},
  year = {1983},
  editor = {Boas, Mary L.},
  author = {Boas, Mary L.},
  edition = {2},
  owner = {godin}
}

@ARTICLE{Bodenstein86,
  author = {Bodenstein, Lawrence},
  title = {A dynamic simulation model of tissue growth and cell patterning.},
  journal = CDiff,
  year = {1986},
  volume = {19},
  pages = {19--33},
  number = {1},
  month = Jul,
  abstract = {The distributions of cells in tissues of experimental chimaeras and
	mosaics can serve as tests of mechanisms and rules by which single
	cells organize themselves into complex, multicellular structures
	during embryogenesis. We have devised a dynamic, computer simulation
	model of tissue growth and cell patterning which is directly applicable
	to the analysis of chimaeras and mosaics. In the model, schematized
	cells possess a small behavioral repertoire and simple rules for
	the carrying out of these behaviors. Populations of such cells evolve
	tissue patterns in real-time that are very similar to those seen
	in experimental animals. In particular, we have modeled the major
	pattern features seen in amphibian and mammalian eye chimaeras and
	mosaics. We have demonstrated that cell mixing can be a passive concomitant
	of interstitial cell division, a result which alleviates the need
	to postulate active cell mixing in such mammalian systems. We expect
	this approach to be a valuable addition to methods of pattern analysis
	in development.},
  doi = {10.1016/0045-6039(86)90022-9},
  keywords = {chimaera; cell patterning; clonal growth; computer model; retinal
	pigment epithelium},
  pmid = {3755380}
}

@INBOOK{Boer92,
  chapter = {A model for cellular development in morphogenetic fields},
  pages = {351--370},
  title = {Lindenmayer systems: Impacts on theoretical computer science, computer
	graphics, and developmental biology},
  publisher = {Springer-Verlag New York, Inc.},
  year = {1992},
  editor = {Rozenberg, Grzegorz and Salomaa, Arto},
  author = {de Boer, M. and Fracchia, F. David and Prusinkiewicz, Przemys\l{}aw},
  month = Jun,
  file = {Boer92.pdf:bioinfo/Boer92.pdf:PDF},
  owner = {barbierp},
  timestamp = {2008.08.08}
}

@PHDTHESIS{Boer89,
  author = {de Boer, Martin J. M.},
  title = {Analysis and computer generation of division patterns in cell layers
	using developmental algorithms.},
  school = {University of Utrecht},
  year = {1989},
  booktitle = {Graph grammars and their application to computer science; Fifth International
	Workshop},
  editor = {Rozenberg, G. and Salomaa, A.},
  owner = {barbier},
  pages = {521--535},
  publisher = {Springer-Verlag, Berlin},
  timestamp = {2009.04.05}
}

@ARTICLE{Boer90,
  author = {de Boer, Martin J. M. and de Does, Mark},
  title = {The relationship between cell division pattern and global shape of
	young fern gametophytes. {I}. {A} model study.},
  journal = BZ,
  year = {1990},
  volume = {151},
  pages = {423--434},
  number = {4},
  month = Dec,
  abstract = {We have investigated the relationship between cell division and shape
	in mathematical models of fern gametophyte development. In particular,
	we attempted to infer what properties of cell division patterns are
	responsible for the development of heart-shaped thalli. We focused
	on those types of gametophytes that develop from an initial cell,
	splitting off segments alternately to the left and to the right.
	Computer simulations showed that a heart shape developed when the
	ratio between the rates of anticlinal and periclinal divisions in
	segments (the division ratio) was below a certain threshold. In the
	computer simulations we used map L-systems for the generation of
	cell division patterns and a center-of-gravity algorithm for the
	computation of cell shapes. The division ratio provided a quantitative
	characterization of the tendency of the cell division pattern to
	develop a heart shape. Together with map DOL-systems it can be applied
	to real gametophytes to investigate their morphogenesis.},
  bdsk-url-1 = {http://www.jstor.org/stable/2995329},
  file = {Boer90.pdf:bioinfo/Boer90.pdf:PDF},
  owner = {barbierp},
  timestamp = {2009.04.08},
  url = {http://www.jstor.org/stable/2995329}
}

@BOOK{Boissonnat95,
  title = {G\'{e}om\'{e}trie algorithmique},
  publisher = {Ediscience international},
  year = {1995},
  editor = {Puech, Claude and Rifflet, Jean-Marie},
  author = {Boissonnat, Jean-Daniel and Yvinec, Mariette}
}

@BOOK{Bollobas98,
  title = {Modern graph theory},
  publisher = {Springer},
  year = {1998},
  author = {B\'{e}la Bollob\'{a}s},
  series = {Graduate texts in mathematics},
  abstract = {The time has now come when graph theory should be part of the education
	of every serious student of mathematics and computer science, both
	for its own sake and to enhance the appreciation of mathematics as
	a whole. This book is an in-depth account of graph theory reflecting
	the current state of the subject and emphasizing connections with
	other branches of pure mathematics. The volume grew out of the author's
	earlier book, Graph Theory: An Introductory Course, but its length
	is well over twice that of its predecessor, allowing it to reveal
	many exciting new developments in the subject.In addition to a modern
	treatment of the classical areas of graph theory such as coloring,
	matching, extremal theory, and algebraic graph theory, the book presents
	a detailed account of newer topics, including Szemeredi's Regularity
	Lemma and its use, Shelah's extension of the Hales-Jewett Theorem,
	the precise nature of the phase transition in a random graph process,
	the connection between electrical networks and random walks on graphs,
	and the Tutte polynomial and its cousins in knot theory.In no other
	branch of mathematics is it as vital to tackle and solve challenging
	exercises in order to master the subject. To this end, the book contains
	an unusually large number of well thought-out exercises: over 600
	in total.},
  bdsk-url-1 = {http://books.google.com/books?hl=fr&lr=&id=rjOLbPR3SIkC&oi=fnd&pg=RA2-PA1&sig=lsjjJCnVYIfWHr8T6zkwWFcfZQo&dq=Bollobas+1998#PPP1,M1},
  owner = {barbier},
  timestamp = {2007.01.15},
  url = {http://books.google.com/books?hl=fr&lr=&id=rjOLbPR3SIkC&oi=fnd&pg=RA2-PA1&sig=lsjjJCnVYIfWHr8T6zkwWFcfZQo&dq=Bollobas+1998#PPP1,M1}
}

@MANUAL{Boudon01,
  title = {{GEOM} module manual: {I} user guide},
  author = {Boudon, Fr\'{e}d\'{e}ric and Nouguier, Christophe and Godin, Christophe},
  organization = {CIRAD},
  month = mar,
  year = {2001}
}

@MANUAL{Boudon01a,
  title = {{GEOM} module manual: {II} developer guide},
  author = {Boudon, Fr\'{e}d\'{e}ric and Nouguier, Christophe and Godin, Christophe},
  organization = {CIRAD},
  month = apr,
  year = {2001}
}

@ARTICLE{Boutte06,
  author = {Boutt\'{e}, Yohann and Crosnier, Marie-Th\'{e}r\`{e}se and Carraro,
	Nicola and Traas, Jan and Satiat-Jeunemaitre, B\'{e}atrice},
  title = {The plasma membrane recycling pathway and cell polarity in plants:
	studies on PIN proteins.},
  journal = JCS,
  year = {2006},
  volume = {119},
  pages = {1255--1265},
  number = {Pt 7},
  month = Apr,
  abstract = {The PIN-FORMED (PIN) proteins are plasma-membrane-associated facilitators
	of auxin transport. They are often targeted to one side of the cell
	only through subcellular mechanisms that remain largely unknown.
	Here, we have studied the potential roles of the cytoskeleton and
	endomembrane system in the localisation of PIN proteins. Immunocytochemistry
	and image analysis on root cells from Arabidopsis thaliana and maize
	showed that 10-30\% of the intracellular PIN proteins mapped to the
	Golgi network, but never to prevacuolar compartments. The remaining
	70-90\% were associated with yet to be identified structures. The
	maintenance of PIN proteins at the plasma membrane depends on a BFA-sensitive
	machinery, but not on microtubules and actin filaments. The polar
	localisation of PIN proteins at the plasmamembrane was not reflected
	by any asymmetric distribution of cytoplasmic organelles. In addition,
	PIN proteins were inserted in a symmetrical manner at both sides
	of the cell plate during cytokinesis. Together, the data indicate
	that the localisation of PIN proteins is a postmitotic event, which
	depends on local characteristics of the plasma membrane and its direct
	environment. In this context, we present evidence that microtubule
	arrays might define essential positional information for PIN localisation.
	This information seems to require the presence of an intact cell
	wall.},
  doi = {10.1242/jcs.02847},
  file = {Boutte06.pdf:bioinfo/Boutte06.pdf:PDF},
  institution = {Laboratoire de Dynamique de la Compartimentation Cellulaire, Institut
	des Sciences du V{\'e}g{\'e}tal, CNRS UPR2355, 9 Gif-sur-Yvette CEDEX,
	France.},
  keywords = {Arabidopsis Proteins, genetics/metabolism; Arabidopsis, anatomy /&/
	histology/cytology/drug effects/genetics/growth /&/ development/metabolism;
	Blotting, Western; Brefeldin A, pharmacology; Carbocyanines; Cell
	Membrane, drug effects/metabolism; Cell Polarity; Dose-Response Relationship,
	Drug; Fluorescein-5-isothiocyanate; Fluorescent Antibody Technique;
	Fluorescent Dyes; Immunohistochemistry; Microscopy, Confocal; Models,
	Biological; Mutation; Plant Proteins, genetics/metabolism; Plant
	Roots, cytology/drug effects; Zea mays, cytology/drug effects/genetics/growth
	/&/ development/metabolism},
  owner = {barbierp},
  pii = {jcs.02847},
  pmid = {16522683},
  timestamp = {2008.12.08}
}

@ARTICLE{Brand00,
  author = {Brand, Ulrike and Fletcher, Jennifer C. and Hobe, Martin and Meyerowitz,
	Elliot M. and Simon, R\"{u}diger},
  title = {Dependence of stem cell fate in {{\itshape Arabidopsis}} on a feedback
	loop regulated by {{\itshape CLV3}} activity},
  journal = {Science},
  year = {2000},
  volume = {289},
  pages = {617--619},
  file = {:biology/Brand00.pdf:PDF}
}

@ARTICLE{Braun35,
  author = {Braun, Alexander},
  title = {Dr. {S}chimper's {V}ortrage \"{u}ber die {M}oglichkeit eines wissenschaftlichen
	{V}erstandnisses der {B}lattstellung \ldots {F}lora.},
  journal = {Iena},
  year = {1835},
  volume = {18},
  pages = {145--191},
  owner = {barbier}
}

@ARTICLE{Braun31,
  author = {Braun, Alexander},
  title = {Vergleichende {U}ntersuchung \"{u}ber die {O}rdnung der {S}chuppen
	an den {T}annenzapfen : als {E}inleitung zur {U}ntersuchung der {B}lattstellung
	berhaupt.},
  journal = NAACLC,
  year = {1831},
  volume = {15},
  pages = {195--402},
  owner = {barbier}
}

@ARTICLE{Bravais39,
  author = {Bravais, Louis and Bravais, Auguste},
  title = {Essaie sur la disposition des feuilles rectis\'{e}ri\'{e}es.},
  journal = ASN,
  year = {1839},
  volume = {12},
  pages = {5--14 \& 65--77},
  number = {2},
  owner = {barbier}
}

@ARTICLE{Bravais37,
  author = {Bravais, Louis and Bravais, Auguste},
  title = {Essai sur la disposition des feuilles curvis\'{e}ri\'{e}es},
  journal = ASN,
  year = {1837},
  volume = {7},
  pages = {42--110}
}

@ARTICLE{Bravais37a,
  author = {Bravais, Louis and Bravais, Auguste},
  title = {Essai sur la disposition sym\'{e}trique des inflorescences},
  journal = ASN,
  year = {1837},
  volume = {8},
  pages = {11--42}
}

@ARTICLE{Byrne00,
  author = {Byrne, Mary E. and Barley, Ross and Curtis, Mark and Arroyo, Juana
	Maria and Dunham, Maitreya and Hudson, Andrew and Martienssen, Robert
	A.},
  title = {{{\itshape Asymmetric leaves1}} mediates leaf patterning and stem
	cell function in {A}rabidopsis},
  journal = {Nature},
  year = {2000},
  volume = {408},
  pages = {967--971},
  file = {:biology/Byrne00.pdf:PDF}
}

